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Chromosome 9

ChrPosition in a YAC physical map (genetic distance, cM)Marker name 1)Type of marker 2)Enzyme 3)Amplified band size (bp) in Nipponbare5' primer sequence3' primer sequenceMapping populationPosition 4)Comment
90.8C1232CAPSHhaI9005' TTTGGAACTGCCCTTGTG 3' 5' TTAGTGGGAGCGTGTTTT 3'F2C1232
9
E1828STS
2485' GAA TGC CAG AAG AAT AAG TG 3'5' ACA AGC TAA GCA TAA GGC AG 3'BILR1164/R1687
920.7-21.4R1687STS
3305' CCC AAA GAG GCA AAG AG 3'5' AAG CAG CAG ATT TTT ACA CC 3'F2R1687dominant
936R79CAPSHinfI12005' ATC TTA TCG CGT CAT TGA AC 3'5' TTG CCG AGC TTG AAT TAT TG 3'F2R79
945.2-49.3R10143STS
2465' ACG ACG TGA GGT ACC GCT TC 3'5' GGA CAA GAG AAG GGC CCA AC 3'BILR1751
955.9S1974SCAPSHinfI18005' TTG TTC GCC TCC GCT TCT TC 3'5' CTC TCC CAC TAG GCA AAT GT 3'F2S1974S
958.3-60.8C12802STS
1925' AGT TGC AGA GAG GGC TAT TG 3'5' ACA GCG TAG GAA AGA TGA GG 3'BILG385/R2272
962.4S1801CAPSMboI13005' CTA GAA ATG GCA CCG ACT T 3'5' CAT ACC TAC ACG GCT ACA CC 3'F2S1801
963.5-65.1E61552STS
2145' GCT GCT TAG AAT TTC CGG TC 3'5' AAA GGG CAC GGG ATG ACA AG 3'BILR2638
969.5C259BSTS
24005' ACC ACC ACC ACT CCA CCG AT 3'5' GGT TCA ACA TCC CAG TCG CA 3'F2C259B
972.1S1057CAPSMspI,HapII11005' AGA GTA TAC CGC CGC CTA A 3'5' CTG AAC CAG CCC AAC ACT 3'F2S1057
9
S15528STS
2065' CTA TCA CTG GGT TCT GTG TC 3'5' GAA CAT CAC CGA CTA TCA CC 3'BILC609
979.1-82.4E20107STS
2245' CGC CTA CAA CGC CAA GAT CG 3'5' TCG CAA ATC AAC ACC ATT AC 3'BILC1263dominant
990.4C506CAPSPstI,HaeIII,MspI,HapII,SacII16005' GCT TCG CCG CTT GAT AAA 3'5' TCA TTA AAC AGG ATG CAA GAG A 3'F2C506
990.4-91.5C11021STS
2605' CAG TGG TTA TTG CGG GGA GC 3'5' CCT TCA AAC GTC GAC TCT GC 3'BILC506/G293
9
E21191STS
2275' CCC CTC GCT GAG GCT TAA TC 3'5' TCG GCG GCA TAA AGC TGT AG 3'BILG293
993.5S1456CAPSMboI22005' GGA GGA GAA GGT CAT CAT CG 3'5' CAT CAA CAG TCC AAG CAA CC 3'F2S1456
90R470NP

5' AGG AGG GAG CTG CCG TCT A 3'5' CCG ATC GAG GCG TGC TT 3'


92.1S2662NP
6005' TTT GAT GAG CCT GCG TAG 3'5' CCT TTG AGT TTC GGT CTT G 3'


965.1R2638NP
20005' GTC CAC CTA CCG CTT GTT CC 3'5' CGA GAT TAC AGG ATG CTT CA 3'


968.2R1562NP
5805' CGC CAT TTG ACC TCT TTG AC 3'5' GTT CCT CTT GCC GCT TCT TT 3'


968.2-69.1C846NP
4005' TGA GCT ATT GTT TGG CAA GA 3'5' AAT GCA CAG TTT CGG ATT TC 3'


972.1S14195NP
16005' GGC TCG TGG CTC GTC AA 3'5' CCG GCA AGG TTC GTC ATC T 3'


974.7-76.1C1720NP
12005' GGG TGT ATC ATT GAG GCC AG 3'5' ACT TGT CCA TCA AAA ACG GC 3'


978.5C1263NP
8005' CCA GGA CCC CTT CAG TT 3'5' CAA GAA TGA TTG ATA CTA CAG AAA 3'


984.3C570NP
23005' TCC AGA ACA TGC ACC TTG 3'5' AAA CCT CGC TGC TTC AGT AG 3'


1) Polymorphism between Nipponbare and Kasalath were revealed by STS, CAPS, or dCAPS. NP indicates that no polymorphism was detected between Nipponbare and Kasalath.
2) Restriction enzymes used for CAPS and dCAPS to detect polymorphism between Nipponbare and Kasalath. No digestion is needed for STS markers.
3) Gel electrophoresis images of each marker can be linked at the "marker mane" column.
4) Chromosomal location of each marker is shown by either the RFLP marker co-segregated or the interval of flanking RFLP markers on the previously reported linkage map (Harushima et al. 1998, Lin et al.1998).
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